Starting phenix.real_space_refine on Sun Feb 8 05:55:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hbp_52024/02_2026/9hbp_52024_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hbp_52024/02_2026/9hbp_52024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hbp_52024/02_2026/9hbp_52024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hbp_52024/02_2026/9hbp_52024.map" model { file = "/net/cci-nas-00/data/ceres_data/9hbp_52024/02_2026/9hbp_52024_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hbp_52024/02_2026/9hbp_52024_trim.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 116 5.16 5 C 12970 2.51 5 N 3426 2.21 5 O 3863 1.98 5 H 20146 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40521 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6718 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 27, 'TRANS': 400} Chain breaks: 6 Chain: "B" Number of atoms: 6484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6484 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 26, 'TRANS': 388} Chain breaks: 7 Chain: "E" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1826 Classifications: {'peptide': 122} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "F" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1722 Classifications: {'peptide': 113} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 2 Chain: "G" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1814 Classifications: {'peptide': 119} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain breaks: 3 Chain: "H" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1794 Classifications: {'peptide': 116} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain breaks: 2 Chain: "C" Number of atoms: 6701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 6701 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 27, 'TRANS': 399} Chain breaks: 6 Chain: "D" Number of atoms: 6461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6461 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 26, 'TRANS': 387} Chain breaks: 7 Chain: "I" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1773 Classifications: {'peptide': 118} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain breaks: 1 Chain: "J" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1639 Classifications: {'peptide': 108} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 3 Chain: "K" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1749 Classifications: {'peptide': 115} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain breaks: 3 Chain: "L" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1784 Classifications: {'peptide': 115} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain breaks: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.69, per 1000 atoms: 0.19 Number of scatterers: 40521 At special positions: 0 Unit cell: (175.187, 137.804, 228.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 O 3863 8.00 N 3426 7.00 C 12970 6.00 H 20146 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 490 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 390 " distance=2.02 Simple disulfide: pdb=" SG CYS A 566 " - pdb=" SG CYS A 575 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 490 " distance=2.05 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 390 " distance=1.99 Simple disulfide: pdb=" SG CYS B 566 " - pdb=" SG CYS B 575 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 101 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 101 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS D 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 490 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 390 " distance=2.03 Simple disulfide: pdb=" SG CYS C 566 " - pdb=" SG CYS C 575 " distance=2.03 Simple disulfide: pdb=" SG CYS D 283 " - pdb=" SG CYS D 296 " distance=2.03 Simple disulfide: pdb=" SG CYS D 377 " - pdb=" SG CYS D 490 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 390 " distance=2.03 Simple disulfide: pdb=" SG CYS D 566 " - pdb=" SG CYS D 575 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 101 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 101 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 422 " " NAG B 701 " - " ASN B 422 " " NAG C 701 " - " ASN C 422 " " NAG D 701 " - " ASN D 422 " Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4826 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 41 sheets defined 10.7% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 143 through 149 Processing helix chain 'A' and resid 149 through 178 removed outlier: 3.833A pdb=" N THR A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) Proline residue: A 169 - end of helix removed outlier: 4.094A pdb=" N GLY A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 371 through 380 Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'B' and resid 158 through 177 Proline residue: B 169 - end of helix removed outlier: 4.142A pdb=" N GLY B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 Processing helix chain 'B' and resid 372 through 382 removed outlier: 4.134A pdb=" N CYS B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 531 removed outlier: 4.284A pdb=" N ASP B 531 " --> pdb=" O SER B 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 Processing helix chain 'F' and resid 32 through 38 Processing helix chain 'F' and resid 92 through 96 removed outlier: 3.852A pdb=" N THR F 96 " --> pdb=" O PRO F 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'C' and resid 143 through 149 Processing helix chain 'C' and resid 149 through 167 Processing helix chain 'C' and resid 167 through 177 removed outlier: 3.559A pdb=" N LEU C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 370 through 381 removed outlier: 4.420A pdb=" N GLN C 374 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 381 " --> pdb=" O CYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 392 removed outlier: 4.386A pdb=" N ASN C 391 " --> pdb=" O TYR C 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 178 Proline residue: D 169 - end of helix removed outlier: 4.305A pdb=" N GLY D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 371 through 380 Processing helix chain 'D' and resid 381 through 383 No H-bonds generated for 'chain 'D' and resid 381 through 383' Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 527 through 531 removed outlier: 3.914A pdb=" N ASP D 531 " --> pdb=" O SER D 528 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 96 Processing helix chain 'J' and resid 32 through 38 removed outlier: 4.271A pdb=" N SER J 36 " --> pdb=" O ASP J 32 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.816A pdb=" N LYS K 64 " --> pdb=" O ASP K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'L' and resid 73 through 75 No H-bonds generated for 'chain 'L' and resid 73 through 75' Processing helix chain 'L' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 199 removed outlier: 3.969A pdb=" N LEU A 595 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 561 " --> pdb=" O ARG A 580 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 216 through 224 removed outlier: 5.457A pdb=" N ASN A 218 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU A 233 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 227 " --> pdb=" O SER A 224 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ARG A 249 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL A 273 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE A 251 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR A 271 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE A 253 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 283 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 282 through 283 current: chain 'A' and resid 291 through 297 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 291 through 297 current: chain 'A' and resid 330 through 333 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 330 through 333 current: chain 'A' and resid 358 through 366 Processing sheet with id=AA4, first strand: chain 'A' and resid 438 through 441 removed outlier: 7.214A pdb=" N ILE A 463 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 480 through 481 Processing sheet with id=AA6, first strand: chain 'A' and resid 511 through 512 Processing sheet with id=AA7, first strand: chain 'B' and resid 193 through 199 removed outlier: 4.180A pdb=" N LEU B 595 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE B 561 " --> pdb=" O ARG B 580 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 215 through 216 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 215 through 216 current: chain 'B' and resid 227 through 235 removed outlier: 6.259A pdb=" N PHE B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N THR B 268 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LYS B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU B 266 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 282 through 283 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 282 through 283 current: chain 'B' and resid 291 through 297 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 291 through 297 current: chain 'B' and resid 330 through 333 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 330 through 333 current: chain 'B' and resid 358 through 367 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 422 through 426 current: chain 'B' and resid 448 through 452 removed outlier: 7.063A pdb=" N ILE B 463 " --> pdb=" O HIS B 477 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 480 through 481 Processing sheet with id=AB2, first strand: chain 'B' and resid 511 through 512 Processing sheet with id=AB3, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AB4, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.721A pdb=" N MET E 40 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR E 56 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP E 42 " --> pdb=" O VAL E 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AB6, first strand: chain 'F' and resid 63 through 65 removed outlier: 6.589A pdb=" N TRP F 42 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR F 56 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET F 40 " --> pdb=" O THR F 56 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N CYS F 101 " --> pdb=" O GLN F 113 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLN F 113 " --> pdb=" O CYS F 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'G' and resid 28 through 38 removed outlier: 3.505A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 106 through 107 Processing sheet with id=AB9, first strand: chain 'H' and resid 2 through 6 Processing sheet with id=AC1, first strand: chain 'H' and resid 28 through 38 removed outlier: 7.506A pdb=" N ASN H 32 " --> pdb=" O THR H 52 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N THR H 52 " --> pdb=" O ASN H 32 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 106 through 107 Processing sheet with id=AC2, first strand: chain 'C' and resid 193 through 198 removed outlier: 3.602A pdb=" N PHE C 561 " --> pdb=" O ARG C 580 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLU C 582 " --> pdb=" O PRO C 559 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 216 through 224 removed outlier: 4.487A pdb=" N MET C 219 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR C 231 " --> pdb=" O MET C 219 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR C 221 " --> pdb=" O GLY C 229 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLY C 229 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE C 223 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ARG C 249 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL C 273 " --> pdb=" O ARG C 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE C 251 " --> pdb=" O TYR C 271 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR C 271 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE C 253 " --> pdb=" O THR C 269 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET C 263 " --> pdb=" O TRP C 259 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 282 through 283 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 282 through 283 current: chain 'C' and resid 291 through 297 Processing sheet with id=AC5, first strand: chain 'C' and resid 301 through 303 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 342 through 346 current: chain 'C' and resid 358 through 367 Processing sheet with id=AC6, first strand: chain 'C' and resid 438 through 441 removed outlier: 7.038A pdb=" N ILE C 463 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 480 through 481 Processing sheet with id=AC8, first strand: chain 'C' and resid 511 through 512 Processing sheet with id=AC9, first strand: chain 'D' and resid 193 through 198 removed outlier: 4.142A pdb=" N PHE D 561 " --> pdb=" O ARG D 580 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 216 through 223 removed outlier: 6.626A pdb=" N LEU D 233 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET D 219 " --> pdb=" O THR D 231 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR D 231 " --> pdb=" O MET D 219 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR D 221 " --> pdb=" O GLY D 229 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY D 229 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE D 223 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ARG D 249 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL D 273 " --> pdb=" O ARG D 249 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE D 251 " --> pdb=" O TYR D 271 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR D 271 " --> pdb=" O PHE D 251 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE D 253 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 282 through 283 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 282 through 283 current: chain 'D' and resid 291 through 297 Processing sheet with id=AD3, first strand: chain 'D' and resid 301 through 303 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 342 through 346 current: chain 'D' and resid 358 through 367 Processing sheet with id=AD4, first strand: chain 'D' and resid 350 through 351 removed outlier: 6.194A pdb=" N ARG D 351 " --> pdb=" O TYR D 439 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N GLU D 441 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE D 463 " --> pdb=" O HIS D 477 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 480 through 481 Processing sheet with id=AD6, first strand: chain 'D' and resid 511 through 512 removed outlier: 3.536A pdb=" N TYR D 520 " --> pdb=" O TYR D 539 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.557A pdb=" N VAL I 5 " --> pdb=" O THR I 23 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.785A pdb=" N MET I 40 " --> pdb=" O THR I 56 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR I 56 " --> pdb=" O MET I 40 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP I 42 " --> pdb=" O VAL I 54 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.619A pdb=" N SER J 76 " --> pdb=" O TYR J 85 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.477A pdb=" N GLY J 10 " --> pdb=" O THR J 118 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLN J 113 " --> pdb=" O CYS J 101 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS J 101 " --> pdb=" O GLN J 113 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET J 40 " --> pdb=" O THR J 56 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N THR J 56 " --> pdb=" O MET J 40 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP J 42 " --> pdb=" O VAL J 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL J 54 " --> pdb=" O TRP J 42 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.588A pdb=" N LEU K 18 " --> pdb=" O MET K 82 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 28 through 37 removed outlier: 3.545A pdb=" N ALA K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 106 through 107 Processing sheet with id=AE4, first strand: chain 'L' and resid 2 through 7 removed outlier: 3.734A pdb=" N THR L 77 " --> pdb=" O ASP L 72 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE L 68 " --> pdb=" O GLN L 81 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 28 through 39 removed outlier: 3.680A pdb=" N ALA L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ARG L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 57 through 59 current: chain 'L' and resid 106 through 107 681 hydrogen bonds defined for protein. 1794 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.90 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20140 1.03 - 1.23: 158 1.23 - 1.42: 8509 1.42 - 1.62: 11944 1.62 - 1.81: 176 Bond restraints: 40927 Sorted by residual: bond pdb=" N ILE B 335 " pdb=" CA ILE B 335 " ideal model delta sigma weight residual 1.456 1.492 -0.036 8.60e-03 1.35e+04 1.74e+01 bond pdb=" C ILE C 545 " pdb=" N SER C 546 " ideal model delta sigma weight residual 1.331 1.285 0.046 1.29e-02 6.01e+03 1.27e+01 bond pdb=" N VAL G 94 " pdb=" CA VAL G 94 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.15e-02 7.56e+03 1.12e+01 bond pdb=" N ILE D 216 " pdb=" CA ILE D 216 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.27e-02 6.20e+03 1.09e+01 bond pdb=" N ILE D 217 " pdb=" CA ILE D 217 " ideal model delta sigma weight residual 1.461 1.499 -0.039 1.19e-02 7.06e+03 1.06e+01 ... (remaining 40922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 66336 1.78 - 3.56: 6977 3.56 - 5.34: 428 5.34 - 7.11: 89 7.11 - 8.89: 3 Bond angle restraints: 73833 Sorted by residual: angle pdb=" N PHE B 150 " pdb=" CA PHE B 150 " pdb=" C PHE B 150 " ideal model delta sigma weight residual 112.24 105.88 6.36 1.28e+00 6.10e-01 2.47e+01 angle pdb=" CA ILE B 335 " pdb=" C ILE B 335 " pdb=" O ILE B 335 " ideal model delta sigma weight residual 120.88 117.55 3.33 6.80e-01 2.16e+00 2.41e+01 angle pdb=" N GLY B 457 " pdb=" CA GLY B 457 " pdb=" C GLY B 457 " ideal model delta sigma weight residual 115.36 109.04 6.32 1.33e+00 5.65e-01 2.26e+01 angle pdb=" N ALA G 40 " pdb=" CA ALA G 40 " pdb=" C ALA G 40 " ideal model delta sigma weight residual 112.17 105.93 6.24 1.36e+00 5.41e-01 2.11e+01 angle pdb=" N THR A 393 " pdb=" CA THR A 393 " pdb=" C THR A 393 " ideal model delta sigma weight residual 113.17 107.69 5.48 1.26e+00 6.30e-01 1.89e+01 ... (remaining 73828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 17438 17.66 - 35.32: 1395 35.32 - 52.98: 489 52.98 - 70.64: 121 70.64 - 88.30: 28 Dihedral angle restraints: 19471 sinusoidal: 10682 harmonic: 8789 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 95 " pdb=" CB CYS H 95 " ideal model delta sinusoidal sigma weight residual 93.00 134.95 -41.95 1 1.00e+01 1.00e-02 2.46e+01 dihedral pdb=" CB CYS C 382 " pdb=" SG CYS C 382 " pdb=" SG CYS C 390 " pdb=" CB CYS C 390 " ideal model delta sinusoidal sigma weight residual -86.00 -123.19 37.19 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 95 " pdb=" CB CYS L 95 " ideal model delta sinusoidal sigma weight residual 93.00 59.63 33.37 1 1.00e+01 1.00e-02 1.58e+01 ... (remaining 19468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2576 0.055 - 0.111: 514 0.111 - 0.166: 146 0.166 - 0.221: 13 0.221 - 0.277: 1 Chirality restraints: 3250 Sorted by residual: chirality pdb=" CA CYS B 377 " pdb=" N CYS B 377 " pdb=" C CYS B 377 " pdb=" CB CYS B 377 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA VAL B 459 " pdb=" N VAL B 459 " pdb=" C VAL B 459 " pdb=" CB VAL B 459 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA VAL B 337 " pdb=" N VAL B 337 " pdb=" C VAL B 337 " pdb=" CB VAL B 337 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 3247 not shown) Planarity restraints: 6000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 701 " 0.071 2.00e-02 2.50e+03 5.84e-02 4.26e+01 pdb=" C7 NAG A 701 " -0.024 2.00e-02 2.50e+03 pdb=" C8 NAG A 701 " 0.055 2.00e-02 2.50e+03 pdb=" N2 NAG A 701 " -0.091 2.00e-02 2.50e+03 pdb=" O7 NAG A 701 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 389 " -0.023 2.00e-02 2.50e+03 4.60e-02 2.11e+01 pdb=" C MET B 389 " 0.080 2.00e-02 2.50e+03 pdb=" O MET B 389 " -0.030 2.00e-02 2.50e+03 pdb=" N CYS B 390 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 701 " 0.039 2.00e-02 2.50e+03 3.20e-02 1.28e+01 pdb=" C7 NAG B 701 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG B 701 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG B 701 " -0.050 2.00e-02 2.50e+03 pdb=" O7 NAG B 701 " -0.006 2.00e-02 2.50e+03 ... (remaining 5997 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.92: 269 1.92 - 2.59: 44754 2.59 - 3.26: 118775 3.26 - 3.93: 158036 3.93 - 4.60: 246109 Nonbonded interactions: 567943 Sorted by model distance: nonbonded pdb=" H ARG A 179 " pdb="HG13 VAL A 568 " model vdw 1.247 2.270 nonbonded pdb=" HD2 PHE H 67 " pdb="HD21 LEU H 80 " model vdw 1.433 2.270 nonbonded pdb=" HZ1 LYS B 230 " pdb=" OE2 GLU B 593 " model vdw 1.443 2.450 nonbonded pdb=" HG SER E 17 " pdb=" O MET E 88 " model vdw 1.468 2.450 nonbonded pdb="HD22 LEU B 378 " pdb="HD21 LEU B 403 " model vdw 1.485 2.440 ... (remaining 567938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 148 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 149 through 304 or (resi \ d 313 and (name N or name CA or name C or name O or name CB or name CG or name O \ D1 or name OD2 or name HA or name HB2 or name HB3)) or resid 314 through 483 or \ resid 488 through 551 or (resid 557 and (name N or name CA or name C or name O o \ r name HA2 or name HA3)) or resid 558 through 581 or resid 589 through 701)) selection = (chain 'B' and (resid 148 through 282 or (resid 283 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 284 through 295 or (resid 296 and (name N or name CA or name C or n \ ame O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or re \ sid 297 through 304 or (resid 313 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) \ or resid 314 through 701)) selection = (chain 'C' and ((resid 148 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 149 through 304 or resid \ 313 through 483 or resid 488 through 551 or (resid 557 and (name N or name CA o \ r name C or name O or name HA2 or name HA3)) or resid 558 through 581 or resid 5 \ 89 through 701)) selection = (chain 'D' and (resid 148 through 304 or (resid 313 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name \ HB2 or name HB3)) or resid 314 through 701)) } ncs_group { reference = (chain 'E' and (resid 1 through 24 or (resid 29 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name H \ E1 or name HE2 or name HZ )) or resid 30 through 46 or (resid 51 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or nam \ e HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 \ or name HH22)) or resid 52 through 90 or (resid 96 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name HA or name HB or name H \ G1 or name HG21 or name HG22 or name HG23)) or resid 97 through 119)) selection = (chain 'F' and (resid 1 through 46 or (resid 51 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 52 through 90 or (resid 96 and (name N or name CA or name C or name O or \ name CB or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 o \ r name HG22 or name HG23)) or resid 97 through 119)) selection = (chain 'I' and (resid 1 through 24 or (resid 29 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name H \ E1 or name HE2 or name HZ )) or resid 30 through 90 or (resid 96 and (name N or \ name CA or name C or name O or name CB or name OG1 or name CG2 or name HA or nam \ e HB or name HG1 or name HG21 or name HG22 or name HG23)) or resid 97 through 11 \ 9)) selection = (chain 'J' and (resid 1 through 46 or (resid 51 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 52 through 119)) } ncs_group { reference = (chain 'G' and (resid 1 through 8 or (resid 12 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 \ or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 13 t \ hrough 37 or (resid 38 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA or n \ ame HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE o \ r name HH11 or name HH12 or name HH21 or name HH22)) or resid 46 through 123)) selection = (chain 'H' and (resid 1 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name HA2 or name HA3)) or resid 17 through 37 or (resid 38 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name CZ or name NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG \ 2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or na \ me HH21 or name HH22)) or resid 46 through 84 or resid 87 through 123)) selection = (chain 'K' and (resid 1 through 8 or (resid 12 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 \ or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 13 t \ hrough 123)) selection = (chain 'L' and (resid 1 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name HA2 or name HA3)) or resid 17 through 37 or (resid 38 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name CZ or name NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG \ 2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or na \ me HH21 or name HH22)) or resid 46 through 84 or resid 87 through 123)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.260 Extract box with map and model: 0.880 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 36.610 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20810 Z= 0.264 Angle : 0.726 8.893 28267 Z= 0.435 Chirality : 0.050 0.277 3250 Planarity : 0.005 0.058 3573 Dihedral : 14.494 88.300 7601 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.84 % Allowed : 8.29 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.16), residues: 2502 helix: 0.79 (0.38), residues: 204 sheet: -0.13 (0.16), residues: 988 loop : -1.79 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 19 TYR 0.014 0.001 TYR B 520 PHE 0.016 0.001 PHE B 199 TRP 0.029 0.002 TRP A 449 HIS 0.008 0.001 HIS D 350 Details of bonding type rmsd covalent geometry : bond 0.00457 (20781) covalent geometry : angle 0.72235 (28205) SS BOND : bond 0.00932 ( 25) SS BOND : angle 1.26552 ( 50) hydrogen bonds : bond 0.21071 ( 681) hydrogen bonds : angle 9.19735 ( 1794) link_NAG-ASN : bond 0.00504 ( 4) link_NAG-ASN : angle 2.91429 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 621 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8796 (mp) cc_final: 0.8365 (tt) REVERT: A 218 ASN cc_start: 0.8304 (m-40) cc_final: 0.7227 (t0) REVERT: A 278 SER cc_start: 0.8620 (m) cc_final: 0.8339 (p) REVERT: A 331 VAL cc_start: 0.7664 (t) cc_final: 0.7333 (p) REVERT: A 467 SER cc_start: 0.8795 (m) cc_final: 0.8479 (p) REVERT: A 565 GLU cc_start: 0.7792 (tp30) cc_final: 0.7312 (tp30) REVERT: B 197 ARG cc_start: 0.7478 (ttt180) cc_final: 0.6907 (mmm-85) REVERT: B 276 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8153 (mt-10) REVERT: B 427 TYR cc_start: 0.8030 (m-80) cc_final: 0.7570 (m-80) REVERT: B 489 ASN cc_start: 0.8096 (m-40) cc_final: 0.7868 (t0) REVERT: B 549 TYR cc_start: 0.7958 (m-80) cc_final: 0.7177 (m-80) REVERT: E 79 ASN cc_start: 0.7376 (p0) cc_final: 0.7039 (m-40) REVERT: F 67 ASP cc_start: 0.6478 (p0) cc_final: 0.6127 (m-30) REVERT: G 11 LEU cc_start: 0.7288 (mp) cc_final: 0.6914 (tp) REVERT: G 47 LEU cc_start: 0.7900 (tp) cc_final: 0.7449 (tt) REVERT: G 111 ASN cc_start: 0.7947 (t0) cc_final: 0.7312 (m110) REVERT: C 374 GLN cc_start: 0.4558 (mp10) cc_final: 0.4135 (tp40) REVERT: C 411 LEU cc_start: 0.7162 (tp) cc_final: 0.6902 (tt) REVERT: C 427 TYR cc_start: 0.3113 (m-80) cc_final: 0.2843 (m-80) REVERT: D 153 TYR cc_start: 0.5962 (m-10) cc_final: 0.4624 (t80) REVERT: D 262 ASP cc_start: 0.6560 (m-30) cc_final: 0.6333 (m-30) REVERT: D 315 ILE cc_start: 0.4325 (mm) cc_final: 0.4091 (tt) REVERT: D 362 MET cc_start: -0.0472 (mtt) cc_final: -0.0683 (mtm) REVERT: D 403 LEU cc_start: 0.2513 (OUTLIER) cc_final: 0.2287 (mp) REVERT: D 433 ASN cc_start: 0.4187 (t0) cc_final: 0.3167 (m-40) REVERT: D 454 PRO cc_start: 0.2416 (Cg_exo) cc_final: 0.2167 (Cg_endo) REVERT: D 460 LEU cc_start: 0.6413 (mt) cc_final: 0.6176 (mt) REVERT: D 513 LEU cc_start: 0.5164 (pt) cc_final: 0.4746 (pp) REVERT: D 535 VAL cc_start: 0.4335 (t) cc_final: 0.3939 (t) REVERT: D 571 ASP cc_start: 0.7198 (p0) cc_final: 0.6840 (m-30) REVERT: J 31 MET cc_start: 0.2963 (mtt) cc_final: 0.1760 (tpp) REVERT: L 75 LYS cc_start: 0.7826 (ttpp) cc_final: 0.7486 (mttt) outliers start: 19 outliers final: 8 residues processed: 635 average time/residue: 0.3686 time to fit residues: 344.2664 Evaluate side-chains 328 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 319 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 ASN A 516 GLN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS D 371 GLN D 509 ASN I 89 ASN ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN J 79 ASN K 32 ASN L 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.159292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.149325 restraints weight = 113808.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.148855 restraints weight = 202573.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.148196 restraints weight = 193273.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.147731 restraints weight = 165907.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.147737 restraints weight = 149551.677| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20810 Z= 0.232 Angle : 0.661 6.926 28267 Z= 0.348 Chirality : 0.048 0.158 3250 Planarity : 0.005 0.059 3573 Dihedral : 5.103 34.527 2894 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.91 % Favored : 93.01 % Rotamer: Outliers : 0.09 % Allowed : 3.93 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.16), residues: 2502 helix: 1.17 (0.38), residues: 213 sheet: -0.08 (0.16), residues: 994 loop : -1.82 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 100 TYR 0.024 0.002 TYR D 406 PHE 0.022 0.002 PHE B 567 TRP 0.014 0.002 TRP C 449 HIS 0.006 0.002 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00550 (20781) covalent geometry : angle 0.65991 (28205) SS BOND : bond 0.00378 ( 25) SS BOND : angle 0.85248 ( 50) hydrogen bonds : bond 0.04450 ( 681) hydrogen bonds : angle 6.70996 ( 1794) link_NAG-ASN : bond 0.00573 ( 4) link_NAG-ASN : angle 1.68907 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 378 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8106 (m-40) cc_final: 0.7372 (t0) REVERT: B 163 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7861 (mt) REVERT: B 218 ASN cc_start: 0.8137 (m-40) cc_final: 0.7725 (m-40) REVERT: B 277 ASN cc_start: 0.7364 (t0) cc_final: 0.6419 (t0) REVERT: E 11 VAL cc_start: 0.5798 (t) cc_final: 0.5549 (t) REVERT: E 116 GLN cc_start: 0.6238 (tm-30) cc_final: 0.5551 (tp-100) REVERT: G 111 ASN cc_start: 0.7575 (t0) cc_final: 0.7156 (m110) REVERT: C 261 ASN cc_start: 0.5771 (m-40) cc_final: 0.5428 (t0) REVERT: D 153 TYR cc_start: 0.5544 (m-10) cc_final: 0.4230 (t80) REVERT: D 301 THR cc_start: 0.4442 (m) cc_final: 0.4173 (p) REVERT: D 363 VAL cc_start: 0.2358 (m) cc_final: 0.2124 (m) REVERT: D 433 ASN cc_start: 0.4060 (t0) cc_final: 0.2958 (m-40) REVERT: D 513 LEU cc_start: 0.5141 (pt) cc_final: 0.4715 (pp) REVERT: J 31 MET cc_start: 0.2924 (mtt) cc_final: 0.2013 (tpp) REVERT: L 113 TYR cc_start: 0.3735 (m-80) cc_final: 0.2997 (m-80) outliers start: 2 outliers final: 1 residues processed: 380 average time/residue: 0.3569 time to fit residues: 201.5354 Evaluate side-chains 268 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 266 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 83 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 GLN E 87 GLN I 3 GLN I 89 ASN ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 ASN K 81 GLN K 83 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.154839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.147318 restraints weight = 114662.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.146693 restraints weight = 196311.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.146310 restraints weight = 198879.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.145909 restraints weight = 158700.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.145667 restraints weight = 155223.062| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 20810 Z= 0.290 Angle : 0.682 6.333 28267 Z= 0.363 Chirality : 0.049 0.215 3250 Planarity : 0.006 0.072 3573 Dihedral : 5.407 40.150 2894 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.75 % Favored : 92.13 % Rotamer: Outliers : 0.18 % Allowed : 3.84 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.16), residues: 2502 helix: 0.86 (0.37), residues: 219 sheet: -0.24 (0.16), residues: 975 loop : -2.18 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 19 TYR 0.026 0.002 TYR B 520 PHE 0.024 0.002 PHE B 567 TRP 0.030 0.002 TRP A 449 HIS 0.008 0.002 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00698 (20781) covalent geometry : angle 0.68028 (28205) SS BOND : bond 0.00498 ( 25) SS BOND : angle 1.03453 ( 50) hydrogen bonds : bond 0.04333 ( 681) hydrogen bonds : angle 6.43998 ( 1794) link_NAG-ASN : bond 0.00360 ( 4) link_NAG-ASN : angle 1.60347 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 325 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8193 (m-40) cc_final: 0.7546 (t0) REVERT: B 163 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7841 (mt) REVERT: B 277 ASN cc_start: 0.7332 (t0) cc_final: 0.6582 (t0) REVERT: E 116 GLN cc_start: 0.7065 (tm-30) cc_final: 0.6167 (tp40) REVERT: F 31 MET cc_start: 0.5802 (mtt) cc_final: 0.5571 (mtt) REVERT: G 104 TYR cc_start: 0.8480 (m-80) cc_final: 0.8230 (m-80) REVERT: G 111 ASN cc_start: 0.7667 (t0) cc_final: 0.7268 (m110) REVERT: H 111 ASN cc_start: 0.8311 (t0) cc_final: 0.7958 (m-40) REVERT: C 261 ASN cc_start: 0.5729 (m-40) cc_final: 0.5422 (t0) REVERT: D 153 TYR cc_start: 0.5648 (m-10) cc_final: 0.4138 (t80) REVERT: D 433 ASN cc_start: 0.3948 (t0) cc_final: 0.2976 (m-40) REVERT: D 437 MET cc_start: 0.0988 (mmt) cc_final: 0.0104 (mmt) REVERT: I 35 PHE cc_start: 0.4903 (t80) cc_final: 0.4430 (t80) REVERT: I 40 MET cc_start: 0.2706 (ptp) cc_final: 0.2425 (mtm) REVERT: J 31 MET cc_start: 0.3018 (mtt) cc_final: 0.2182 (tpp) outliers start: 4 outliers final: 1 residues processed: 329 average time/residue: 0.3767 time to fit residues: 185.8501 Evaluate side-chains 241 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 239 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 135 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 239 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 138 optimal weight: 0.0370 chunk 118 optimal weight: 0.7980 chunk 220 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 GLN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.156710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.149277 restraints weight = 114044.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.148438 restraints weight = 195849.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.147939 restraints weight = 212706.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.147494 restraints weight = 168476.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.147028 restraints weight = 189043.755| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20810 Z= 0.127 Angle : 0.544 5.431 28267 Z= 0.284 Chirality : 0.046 0.150 3250 Planarity : 0.005 0.068 3573 Dihedral : 4.843 37.730 2894 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.16), residues: 2502 helix: 1.21 (0.38), residues: 218 sheet: -0.12 (0.16), residues: 966 loop : -2.10 (0.15), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 599 TYR 0.017 0.001 TYR B 520 PHE 0.014 0.001 PHE D 481 TRP 0.010 0.001 TRP A 449 HIS 0.005 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00301 (20781) covalent geometry : angle 0.54308 (28205) SS BOND : bond 0.00377 ( 25) SS BOND : angle 0.80776 ( 50) hydrogen bonds : bond 0.03202 ( 681) hydrogen bonds : angle 5.90231 ( 1794) link_NAG-ASN : bond 0.00326 ( 4) link_NAG-ASN : angle 1.11866 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8170 (m-40) cc_final: 0.7410 (t0) REVERT: B 218 ASN cc_start: 0.7961 (m-40) cc_final: 0.7662 (m-40) REVERT: B 276 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7010 (mm-30) REVERT: B 277 ASN cc_start: 0.7313 (t0) cc_final: 0.6491 (t0) REVERT: E 116 GLN cc_start: 0.7093 (tm-30) cc_final: 0.6257 (tp40) REVERT: G 111 ASN cc_start: 0.7598 (t0) cc_final: 0.7310 (m110) REVERT: H 111 ASN cc_start: 0.8152 (t0) cc_final: 0.7732 (m-40) REVERT: D 153 TYR cc_start: 0.5522 (m-10) cc_final: 0.4179 (t80) REVERT: D 433 ASN cc_start: 0.3714 (t0) cc_final: 0.2712 (m-40) REVERT: D 437 MET cc_start: 0.0882 (mmt) cc_final: 0.0424 (mmt) REVERT: D 513 LEU cc_start: 0.5039 (pt) cc_final: 0.4817 (pp) REVERT: J 31 MET cc_start: 0.2989 (mtt) cc_final: 0.2006 (tpp) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.3641 time to fit residues: 177.7830 Evaluate side-chains 242 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 240 optimal weight: 20.0000 chunk 127 optimal weight: 0.5980 chunk 239 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 214 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN K 81 GLN L 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.154618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.147754 restraints weight = 114161.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.146627 restraints weight = 202897.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.145947 restraints weight = 213591.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.145612 restraints weight = 164373.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.145276 restraints weight = 154149.998| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20810 Z= 0.188 Angle : 0.572 5.295 28267 Z= 0.301 Chirality : 0.047 0.205 3250 Planarity : 0.005 0.065 3573 Dihedral : 4.900 38.799 2894 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.16), residues: 2502 helix: 1.14 (0.39), residues: 219 sheet: -0.13 (0.16), residues: 968 loop : -2.20 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 599 TYR 0.020 0.002 TYR B 520 PHE 0.016 0.001 PHE B 567 TRP 0.015 0.001 TRP A 395 HIS 0.005 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00452 (20781) covalent geometry : angle 0.57121 (28205) SS BOND : bond 0.00360 ( 25) SS BOND : angle 0.83277 ( 50) hydrogen bonds : bond 0.03320 ( 681) hydrogen bonds : angle 5.75955 ( 1794) link_NAG-ASN : bond 0.00275 ( 4) link_NAG-ASN : angle 1.25261 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8169 (m-40) cc_final: 0.7507 (t0) REVERT: B 276 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7043 (mm-30) REVERT: B 277 ASN cc_start: 0.7397 (t0) cc_final: 0.6608 (t0) REVERT: B 367 VAL cc_start: 0.9307 (t) cc_final: 0.8886 (m) REVERT: B 427 TYR cc_start: 0.7835 (m-80) cc_final: 0.7463 (m-80) REVERT: E 116 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6391 (tp40) REVERT: G 111 ASN cc_start: 0.7545 (t0) cc_final: 0.7333 (m110) REVERT: H 111 ASN cc_start: 0.8245 (t0) cc_final: 0.7958 (m-40) REVERT: C 219 MET cc_start: 0.7743 (tmm) cc_final: 0.7530 (ttm) REVERT: D 153 TYR cc_start: 0.5693 (m-10) cc_final: 0.4196 (t80) REVERT: D 433 ASN cc_start: 0.4071 (t0) cc_final: 0.2914 (m-40) REVERT: D 437 MET cc_start: 0.0774 (mmt) cc_final: -0.0301 (mmt) REVERT: J 31 MET cc_start: 0.3281 (mtt) cc_final: 0.2350 (ttt) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.3615 time to fit residues: 163.7972 Evaluate side-chains 231 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 12 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 183 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 199 optimal weight: 20.0000 chunk 186 optimal weight: 0.0030 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN J 79 ASN L 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.155753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.148786 restraints weight = 114621.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.147715 restraints weight = 183963.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.146837 restraints weight = 210275.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.146379 restraints weight = 185113.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.146015 restraints weight = 172970.260| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6030 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20810 Z= 0.130 Angle : 0.532 5.073 28267 Z= 0.277 Chirality : 0.046 0.166 3250 Planarity : 0.005 0.067 3573 Dihedral : 4.662 37.153 2894 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.04 % Allowed : 1.19 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.16), residues: 2502 helix: 1.28 (0.39), residues: 219 sheet: -0.04 (0.16), residues: 972 loop : -2.18 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 72 TYR 0.016 0.001 TYR B 520 PHE 0.015 0.001 PHE D 481 TRP 0.028 0.001 TRP C 449 HIS 0.003 0.001 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00312 (20781) covalent geometry : angle 0.53081 (28205) SS BOND : bond 0.00258 ( 25) SS BOND : angle 0.69436 ( 50) hydrogen bonds : bond 0.03019 ( 681) hydrogen bonds : angle 5.57446 ( 1794) link_NAG-ASN : bond 0.00259 ( 4) link_NAG-ASN : angle 1.09987 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8052 (m-40) cc_final: 0.7417 (t0) REVERT: A 294 SER cc_start: 0.9097 (t) cc_final: 0.8635 (m) REVERT: B 218 ASN cc_start: 0.8265 (m-40) cc_final: 0.8023 (m-40) REVERT: B 276 GLU cc_start: 0.7649 (mt-10) cc_final: 0.6922 (mm-30) REVERT: B 277 ASN cc_start: 0.7399 (t0) cc_final: 0.6615 (t0) REVERT: B 371 GLN cc_start: 0.7162 (tp40) cc_final: 0.5822 (tp40) REVERT: E 116 GLN cc_start: 0.7213 (tm-30) cc_final: 0.6484 (tp-100) REVERT: H 111 ASN cc_start: 0.8145 (t0) cc_final: 0.7871 (m-40) REVERT: D 153 TYR cc_start: 0.5531 (m-10) cc_final: 0.4208 (t80) REVERT: D 433 ASN cc_start: 0.4064 (t0) cc_final: 0.2943 (m-40) REVERT: D 437 MET cc_start: 0.0776 (mmt) cc_final: 0.0486 (mmt) REVERT: J 31 MET cc_start: 0.3363 (mtt) cc_final: 0.2364 (ttt) REVERT: L 113 TYR cc_start: 0.4129 (m-80) cc_final: 0.3688 (m-80) outliers start: 1 outliers final: 0 residues processed: 292 average time/residue: 0.3622 time to fit residues: 162.9346 Evaluate side-chains 233 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 201 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 17 optimal weight: 0.0670 chunk 239 optimal weight: 7.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN I 3 GLN L 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.155818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.146274 restraints weight = 113954.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.145447 restraints weight = 193087.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.144657 restraints weight = 197494.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.143991 restraints weight = 151168.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.143249 restraints weight = 170949.784| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6097 moved from start: 0.6147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20810 Z= 0.118 Angle : 0.522 5.161 28267 Z= 0.273 Chirality : 0.046 0.149 3250 Planarity : 0.005 0.072 3573 Dihedral : 4.524 35.178 2894 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.16), residues: 2502 helix: 1.40 (0.39), residues: 218 sheet: 0.00 (0.17), residues: 954 loop : -2.13 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 66 TYR 0.018 0.001 TYR B 427 PHE 0.016 0.001 PHE D 481 TRP 0.012 0.001 TRP C 449 HIS 0.005 0.001 HIS D 576 Details of bonding type rmsd covalent geometry : bond 0.00283 (20781) covalent geometry : angle 0.52103 (28205) SS BOND : bond 0.00318 ( 25) SS BOND : angle 0.62487 ( 50) hydrogen bonds : bond 0.02920 ( 681) hydrogen bonds : angle 5.44087 ( 1794) link_NAG-ASN : bond 0.00250 ( 4) link_NAG-ASN : angle 1.07062 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8037 (m-40) cc_final: 0.7399 (t0) REVERT: A 294 SER cc_start: 0.9119 (t) cc_final: 0.8723 (m) REVERT: B 218 ASN cc_start: 0.8223 (m-40) cc_final: 0.8004 (m-40) REVERT: B 276 GLU cc_start: 0.7595 (mt-10) cc_final: 0.6764 (mm-30) REVERT: B 277 ASN cc_start: 0.7411 (t0) cc_final: 0.6610 (t0) REVERT: B 371 GLN cc_start: 0.7088 (tp40) cc_final: 0.5772 (tp40) REVERT: E 116 GLN cc_start: 0.7246 (tm-30) cc_final: 0.6366 (tp40) REVERT: D 153 TYR cc_start: 0.5574 (m-10) cc_final: 0.4140 (t80) REVERT: D 433 ASN cc_start: 0.4122 (t0) cc_final: 0.2996 (m-40) REVERT: I 35 PHE cc_start: 0.4556 (t80) cc_final: 0.4128 (t80) REVERT: J 31 MET cc_start: 0.3411 (mtt) cc_final: 0.2259 (ttt) REVERT: L 113 TYR cc_start: 0.4143 (m-80) cc_final: 0.3912 (m-80) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.3400 time to fit residues: 152.5330 Evaluate side-chains 237 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 34 optimal weight: 0.0870 chunk 146 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.155954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.148393 restraints weight = 113669.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.148267 restraints weight = 181663.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.147949 restraints weight = 159951.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.147132 restraints weight = 167568.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.146947 restraints weight = 167063.358| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20810 Z= 0.116 Angle : 0.516 5.174 28267 Z= 0.268 Chirality : 0.046 0.149 3250 Planarity : 0.005 0.075 3573 Dihedral : 4.424 32.448 2894 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.17), residues: 2502 helix: 1.44 (0.39), residues: 218 sheet: 0.01 (0.17), residues: 958 loop : -2.13 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 45 TYR 0.019 0.001 TYR B 427 PHE 0.019 0.001 PHE C 353 TRP 0.020 0.001 TRP D 395 HIS 0.003 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00280 (20781) covalent geometry : angle 0.51508 (28205) SS BOND : bond 0.00246 ( 25) SS BOND : angle 0.74208 ( 50) hydrogen bonds : bond 0.02861 ( 681) hydrogen bonds : angle 5.29007 ( 1794) link_NAG-ASN : bond 0.00233 ( 4) link_NAG-ASN : angle 1.08043 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8079 (m-40) cc_final: 0.7440 (t0) REVERT: B 276 GLU cc_start: 0.7558 (mt-10) cc_final: 0.6745 (mm-30) REVERT: B 277 ASN cc_start: 0.7367 (t0) cc_final: 0.6562 (t0) REVERT: B 371 GLN cc_start: 0.6800 (tp40) cc_final: 0.5481 (tp40) REVERT: D 153 TYR cc_start: 0.5449 (m-10) cc_final: 0.4058 (t80) REVERT: D 433 ASN cc_start: 0.4005 (t0) cc_final: 0.2903 (m-40) REVERT: I 35 PHE cc_start: 0.4326 (t80) cc_final: 0.3861 (t80) REVERT: J 31 MET cc_start: 0.3344 (mtt) cc_final: 0.2274 (ttt) REVERT: L 113 TYR cc_start: 0.4116 (m-80) cc_final: 0.3914 (m-80) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.3330 time to fit residues: 143.2067 Evaluate side-chains 226 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 126 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 184 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 GLN L 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.153383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.146023 restraints weight = 114141.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.145483 restraints weight = 176747.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.145033 restraints weight = 177892.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.144448 restraints weight = 156641.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.143964 restraints weight = 174976.984| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.6677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20810 Z= 0.211 Angle : 0.595 5.754 28267 Z= 0.314 Chirality : 0.047 0.150 3250 Planarity : 0.005 0.076 3573 Dihedral : 4.908 35.256 2894 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.11 % Favored : 90.81 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.16), residues: 2502 helix: 1.08 (0.39), residues: 218 sheet: -0.26 (0.16), residues: 1014 loop : -2.34 (0.16), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 66 TYR 0.028 0.002 TYR B 520 PHE 0.019 0.002 PHE D 481 TRP 0.016 0.002 TRP D 395 HIS 0.006 0.001 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00508 (20781) covalent geometry : angle 0.59327 (28205) SS BOND : bond 0.00418 ( 25) SS BOND : angle 0.99260 ( 50) hydrogen bonds : bond 0.03402 ( 681) hydrogen bonds : angle 5.58207 ( 1794) link_NAG-ASN : bond 0.00235 ( 4) link_NAG-ASN : angle 1.39877 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8188 (m-40) cc_final: 0.7648 (t0) REVERT: B 218 ASN cc_start: 0.8114 (m-40) cc_final: 0.7701 (m-40) REVERT: B 276 GLU cc_start: 0.7563 (mt-10) cc_final: 0.6774 (mm-30) REVERT: B 277 ASN cc_start: 0.7425 (t0) cc_final: 0.6700 (t0) REVERT: B 371 GLN cc_start: 0.6811 (tp40) cc_final: 0.5689 (tp40) REVERT: B 549 TYR cc_start: 0.8488 (m-80) cc_final: 0.8226 (m-80) REVERT: G 104 TYR cc_start: 0.8546 (m-80) cc_final: 0.8207 (m-80) REVERT: D 153 TYR cc_start: 0.5649 (m-10) cc_final: 0.4060 (t80) REVERT: D 433 ASN cc_start: 0.4520 (t0) cc_final: 0.3113 (m-40) REVERT: J 31 MET cc_start: 0.3709 (mtt) cc_final: 0.2255 (ttt) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.3409 time to fit residues: 144.1753 Evaluate side-chains 228 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 136 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 227 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 ASN L 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.154342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.146753 restraints weight = 113549.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.146292 restraints weight = 180455.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.145794 restraints weight = 169014.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.145341 restraints weight = 184795.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.145200 restraints weight = 161852.907| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.6786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20810 Z= 0.139 Angle : 0.538 5.378 28267 Z= 0.281 Chirality : 0.046 0.152 3250 Planarity : 0.005 0.077 3573 Dihedral : 4.642 34.129 2894 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.83 % Favored : 93.09 % Rotamer: Outliers : 0.04 % Allowed : 0.04 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.17), residues: 2502 helix: 1.26 (0.39), residues: 218 sheet: -0.23 (0.16), residues: 988 loop : -2.30 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 543 TYR 0.020 0.001 TYR B 520 PHE 0.017 0.001 PHE D 481 TRP 0.011 0.001 TRP A 395 HIS 0.004 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00334 (20781) covalent geometry : angle 0.53725 (28205) SS BOND : bond 0.00296 ( 25) SS BOND : angle 0.71246 ( 50) hydrogen bonds : bond 0.02975 ( 681) hydrogen bonds : angle 5.39693 ( 1794) link_NAG-ASN : bond 0.00234 ( 4) link_NAG-ASN : angle 1.17848 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8025 (m-40) cc_final: 0.7512 (t0) REVERT: B 218 ASN cc_start: 0.7965 (m-40) cc_final: 0.7751 (m-40) REVERT: B 276 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6725 (mm-30) REVERT: B 277 ASN cc_start: 0.7256 (t0) cc_final: 0.6511 (t0) REVERT: B 371 GLN cc_start: 0.6779 (tp40) cc_final: 0.5515 (tp40) REVERT: B 435 ASP cc_start: 0.7885 (m-30) cc_final: 0.7622 (m-30) REVERT: D 153 TYR cc_start: 0.5644 (m-10) cc_final: 0.4036 (t80) REVERT: D 433 ASN cc_start: 0.4348 (t0) cc_final: 0.3036 (m-40) REVERT: J 31 MET cc_start: 0.3665 (mtt) cc_final: 0.2195 (ttt) outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.3258 time to fit residues: 138.4358 Evaluate side-chains 223 residues out of total 2267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 101 optimal weight: 3.9990 chunk 238 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 210 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.153914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.144096 restraints weight = 114068.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.143210 restraints weight = 199698.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.142049 restraints weight = 198384.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.141262 restraints weight = 193805.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.141128 restraints weight = 164733.232| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.6949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20810 Z= 0.148 Angle : 0.538 5.924 28267 Z= 0.281 Chirality : 0.046 0.150 3250 Planarity : 0.005 0.077 3573 Dihedral : 4.605 34.036 2894 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.39 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.17), residues: 2502 helix: 1.28 (0.39), residues: 219 sheet: -0.30 (0.16), residues: 997 loop : -2.32 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 519 TYR 0.021 0.001 TYR B 520 PHE 0.017 0.001 PHE D 481 TRP 0.020 0.001 TRP D 395 HIS 0.004 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00360 (20781) covalent geometry : angle 0.53691 (28205) SS BOND : bond 0.00315 ( 25) SS BOND : angle 0.74842 ( 50) hydrogen bonds : bond 0.02967 ( 681) hydrogen bonds : angle 5.34786 ( 1794) link_NAG-ASN : bond 0.00224 ( 4) link_NAG-ASN : angle 1.20137 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6371.63 seconds wall clock time: 109 minutes 29.33 seconds (6569.33 seconds total)